VMD-L Mailing List

From: oguz gurbulak (gurbulakoguz_at_REMOVE_yahoo.com)
Date: Sat Apr 11 2015 - 04:51:38 CDT

Dear John Stone,

You can reach the namd log file from the link below. Thanks for your help.

Regards.

http://www.filedropper.com/namd

     On Saturday, April 11, 2015 12:31 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
   

 Hi,
  We would also need a copy of the NAMD log file that fails to be able
to debug the code further.

Cheers,
  John

On Wed, Apr 08, 2015 at 06:50:47AM +0000, oguz gurbulak wrote:
>    Dear John Stone,
>
>    I changed "TOTAL2" in the script with "POTENTIAL" and tried to run it
>    again. It computed the average values of TOTAL, TEMP, PRESSAVG and VOLUME
>    for my first namd out file. But ıt couldn't work for my second out file.
>    I couldn't find where I got the script but  I attached  "namdstats.tcl" I
>    used. Could you please help me to fix the script ?
>
>    Regards.
>    >Main< (A) 50 % source namdstats.tcl
>    Usage: data_avg <logfile> [<first timestep> <last timestep>]
>      <first timestep> and <last timestep> may be entered as numbers or
>      <first timestep> = 'first' will start at the beginning of the
>    simulation
>      <last timestep> = 'last' will go to the end of the simulation
>    Usage: data_time <data stream> <logfile> [<first timestep> <last
>    timestep>]
>      <data stream> = BOND, ANGLE, DIHED, IMPRP, ELECT, VDW, BOUNDARY, MISC,
>    KINETIC, TOTAL, TEMP, POTENTIAL, TOTAL3, TEMPAVG
>    >Main< (A) 51 % data_avg minmd_NPT.out
>    Calculating averages...
>    CALCULATING DATA FROM TIMESTEP 0 TO 999500:
>    BOND: 4108.828256906084
>    ANGLE: 2153.6935096991397
>    DIHED: 0.0
>    IMPRP: 0.0
>    ELECT: -116970.09206833366
>    VDW: 21827.24498616304
>    BOUNDARY: 0.0
>    MISC: 0.0
>    KINETIC: 2067.3828981303786
>    TOTAL: -86812.94240436761
>    TEMP: 49.15447203906191
>    POTENTIAL: -88880.32530247286
>    TOTAL3: -86809.55005141706
>    TEMPAVG: 49.14564788415001
>    PRESSURE: -487.6260775561439
>    GPRESSURE: -368.2150356731323
>    VOLUME: 211735.6768608377
>    PRESSAVG: -485.595377881658
>    GPRESSAVG: -367.8875202654034
>
>    >Main< (A) 52 % data_avg md_NPT.out
>    Calculating averages...
>    can't read "ts(0)": no such variable
>    >Main< (A) 53 %
>
>    On Monday, April 6, 2015 7:58 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>    Hi,
>      You didn't say where you obtained your "namdstats.tcl" script from, so
>    it is hard to guess what might be wrong with the version you have.
>    Google shows that there are several versions of this script floating
>    around.
>    You may have an old one that has not been corrected for the most recent
>    vesions of NAMD.  The current versions of NAMD no longer emit a field
>    named "TOTAL2", it now emits "POTENTIAL" instead.  This breaks scripts
>    that are expect to read "TOTAL2" and don't have any fallback code if it's
>    not there.  I assume that your namdstats.tcl script tries to read TOTAL2,
>    so you may want to try and replace "TOTAL2" in the script with "POTENTIAL"
>    and see if it cures your problem or not.  If not, then you'll need tell us
>    where you got the script and/or who wrote it and we'll help them get it
>    fixed.
>
>    Cheers,
>      John Stone
>      [1]vmd_at_ks.uiuc.edu
>    On Sun, Apr 05, 2015 at 09:54:50PM +0000, oguz gurbulak wrote:
>    > DearAll,
>    >
>    >
>    >
>    > Iwanted to compute the average values of TOTAL, TEMP, PRESSAVG and
>    VOLUME withusing ???namdstats.tcl??? script for a NPT run. But I got
>    theerror ???can't read "ts(0)": no such variable???.How can I solve this
>    problem ? Could you please help me about this issue ?
>    >
>    >
>    >
>    > Regards.
>    >
>    >
>    >  >Main< (A) % source namdstats.tclUsage: data_avg <logfile>[<first
>    timestep> <last timestep>]
>    >
>    >    <first timestep> and<last timestep> may be entered as numbers or
>    >
>    >    <first timestep> ='first' will start at the beginning of the
>    simulation
>    >
>    >    <last timestep> ='last' will go to the end of the simulation
>    >
>    > Usage: data_time <data stream><logfile> [<first timestep> <last
>    timestep>]
>    >
>    >    <data stream> = BOND,ANGLE, DIHED, IMPRP, ELECT, VDW, BOUNDARY, MISC,
>    KINETIC, TOTAL, TEMP, TOTAL2,TOTAL3, TEMPAVG
>    >
>    > >Main< (A)  % data_avg namd_1.out Calculating averages...
>    >
>    > can't read "ts(0)": no suchvariable
>    >
>    > >Main< (A)  %
>    >
>    >
>
>    --
>    NIH Center for Macromolecular Modeling and Bioinformatics
>    Beckman Institute for Advanced Science and Technology
>    University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>    [2]http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
>    [3]http://www.ks.uiuc.edu/Research/vmd/
>
>
> References
>
>    Visible links
>    1. mailto:vmd_at_ks.uiuc.edu
>    2. http://www.ks.uiuc.edu/~johns/
>    3. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/